AMBER Archive (2008)

Subject: RE: AMBER: Dihedral Angle Parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jun 26 2008 - 17:18:52 CDT

Hi Ilyas,

You can have as many terms for a single dihedral as you want as long as they
all differ in the value of the periodicity (n). Effectively you can think of
this as a truncated fourier series, so in theory you can draw any potential
shape you want if you add enough dihedral terms together with varying phase
and periodicities. In terms of implementation of the AMBER force field the
code simply calculates the value of the dihedral term for whatever the
current dihedral angle happens to be so you are free to put in any values
you want, just as long as 'n' is a different integer for each one.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Ilyas Yildirim
> Sent: Thursday, June 26, 2008 3:08 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Dihedral Angle Parameters
>
> Dear Carlos,
>
> Yes, I mean symmetry about 0. For instance the alfa-dihedral angle for the
> RNA is defined with the following parameters:
>
> OS-P -OS-CT 1 0.25 0.0 -3.
> JCC,7,(1986),230
> OS-P -OS-CT 1 1.20 0.0 2. gg&gt
> ene.631g*/mp2
>
> The E_torsion energy function for this dihedral is symmetric about 0. If I
> add another paramater list for this dihedral angle (with a non-zero
> phase), it can become asymetric. However, I am not sure if this is allowed
> in amber force field. Thanks.
>
> Best,
>
> On Thu, 26 Jun 2008, Carlos Simmerling wrote:
>
> > symmetric about what? if still a cosine term, then it has an intrinsic
> symmetry.
> > by varying phases, you can change symmetry about 0 if that's what you
> mean.
> >
> > On Thu, Jun 26, 2008 at 5:07 PM, Ilyas Yildirim
> > <yildirim_at_pas.rochester.edu> wrote:
> > > Dear AMBER users,
> > >
> > > I realized that the amber dihedral parameters are symmetric; the
> torsional
> > > energy vs angle has a symmetric character. Is it reasonable to create
> > > dihedral parameters for a particular dihedral angle such that it will
> have
> > > an asymmetric torsional energy function in amber force field? Thanks
> in
> > > advance.
> > >
> > > Best,
> > >
> > > --
> > > Ilyas Yildirim
> > > ---------------------------------------------------------------
> > > = Department of Physics - =
> > > = University of Rochester - =
> > > = 585-275-6766 (office) - 585-267-5644 (home) =
> > > = http://www.pas.rochester.edu/~yildirim/ =
> > > ---------------------------------------------------------------
> > >
> > > ----------------------------------------------------------------------
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>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Physics - =
> = University of Rochester - =
> = 585-275-6766 (office) - 585-267-5644 (home) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
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